The challenges while building linkage maps for diploid and polyploid species with genotyping-by-sequencing markers

Cristiane Hayumi Taniguti, Jeekin Lau, Antonio Augusto Franco Garcia, Marcelo Mollinari, David Byrne, Oscar Riera-Lizarazu

2023-03-01

Poster presented in the 11th Rosaceae Genomics Conference (Nelson, New Zealand - March 2023)

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References

Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., Da, G., Pereira, S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Franco Garcia, A. A. (n.d.). Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. bioRxiv. https://doi.org/10.1101/2022.11.24.517847

Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242

Margarido, G. R. A., Souza, A. P., & Garcia, A. A. F. (2007). OneMap: software for genetic mapping in outcrossing species. Hereditas, 144(3), 78–79. https://doi.org/10.1111/j.2007.0018-0661.02000.x

Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378

Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6(5), e19379. https://doi.org/10.1371/journal.pone.0019379

Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q., & Buckler, E. S. (2014). TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE, 9(2), 1–11. https://doi.org/10.1371/journal.pone.0090346

Voss, K., Gentry, J., & Auwera, G. van der. (2017). Full-stack genomics pipelining with GATK4+ WDL+ Cromwell [version 1; not peer reviewed]. F1000Research, 4. https://doi.org/10.7490/f1000research.1114631.1

Yu, Z., Du, F., Ban, R., & Zhang, Y. (2020). SimuSCoP: Reliably simulate Illumina sequencing data based on position and context dependent profiles. BMC Bioinformatics, 21(1), 1–18. https://doi.org/10.1186/s12859-020-03665-5

Rivera-Colón, A. G., Rochette, N. C., & Catchen, J. M. (2020). Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Molecular Ecology Resources, March, 1–16. https://doi.org/10.1111/1755- 0998.13163

Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows– Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324

van der Auwera, G., & O’Connor, B. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media, Incorporated. https://books.google.com.br/books?id=wwiCswEACAAJ

Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. ArXiv E-Prints, 9. https://doi.org/1207.3907

Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789–807. https://doi.org/10.1534/genetics.118.301468

Clark, L. v., Lipka, A. E., & Sacks, E. J. (2019). polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. G3: Genes|Genomes|Genetics, 9(March), g3.200913.2018. https://doi.org/10.1534/g3.118.200913

Serang, O., Mollinari, M., & Garcia, A. A. F. (2012). Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids. PLoS ONE, 7(2), 1– 13. https://doi.org/10.1371/journal.pone.0030906

Merkel, D. (2014). Docker : Lightweight Linux Containers for Consistent Development and Deployment Docker : a Little Background Under the Hood. Linux Journal, 2014(239), 2–7.

Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5), e0177459. https://doi.org/10.1371/journal.pone.0177459